RetrogeneDB ID: retro_oruf_26

Retrocopy location

• Organism: Brownbeard rice (Oryza rufipogon)
• Coordinates: 10:10036535..10037282(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ORUFI10G07910
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ORUFI10G17520
• Aliases: None
• Description: None

Sequence

>retro_oruf_26
ATGGCCGCCGCCGCCGCCGGAGGAGGAGGATCACCGGATCACGAGCTGAAGCTGCTCGGCAGCACGAACCCTAGCCCGTT
CGTCACCAGGGTGGAGCTCGCCCTCGCCCTGCGAGGCCTCACCTACGACCTCGTCGCCGTCGACCTCGACCGCAAGACCG
ACCTCCTCCTCGCCGCCAACCCCGTCCACGCCAAGGTCCCCGTCCTCATCCACCGCGGCCGCCCCGTCTGCGAGTCCCGG
GTCATCCTCGAGTACATCGACGACGCCTTCCCCTTCCCCGGCGGCGGCGGCGCCCCGCTCCTCCCCCCCGCCGACGACCC
CCTCGCCCGCGCCGCCGCCCGCTTCTGGGCCGCCCACGTCGACGACGAGTTCGTGGCGTCGTGGAGGCCGGCGTACCTGG
GGAGCACGGAGGGGGAGAGGGCGGAGGGGATGGCGCGGATGGCCGCCGCGGTGGGGGCGCTGGAGGGGGCCCTCGCCGCC
GCGGAGGGGAAGCCCTTCTTCGGCGGCGACGCCCCGGGGCTCGTCGACGTCACGCTGGGGTCGGTGATCCCGCGGACGAG
GGCGAACGAGGCGCTCACGGGGACCAGGGTGCTCGACGCCGCCAGGACGCCGCTGCTGGCGGCGTGGGCGGAGCGGTTCG
GCGAGCTCGACGCCGCCAGGAAGGTGCTCCCGGCCGTCGGCGACGTGGTCGAGTACCTGGAGACGAGGCTCCGGAGGAGT
AATGTGGTTATCGCTAGGAAACAGTAG

Alignment

ORF - retro_oruf_26 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.16 %
• Parental protein coverage: 59.78 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ELKLLGAF-PSAYVTRVELALGFKGLSYEYVKEDLANKSELLLSSNPVHKKVPVLIHNGKPISESQVIVQ
          ELKLLG...PS..VTRVELAL...GL.Y..V..DL..K..LLL..NPVH.KVPVLIH.G.P..ES.VI..
Retrocopy ELKLLGSTNPSPFVTRVELALALRGLTYDLVAVDLDRKTDLLLAANPVHAKVPVLIHRGRPVCESRVILE

Parental  YIDEAFP---GAGVPLLP--SDPYERAVARFWAAYIDDKLLKSWLQASMGKTEEEKAEALKETFAAVANL
          YID.AFP...G.G.PLLP...DP..RA.ARFWAA..DD....SW..A..G.TE.E.AE......AAV..L
Retrocopy YIDDAFPFPGGGGAPLLPPADDPLARAAARFWAAHVDDEFVASWRPAYLGSTEGERAEGMARMAAAVGAL

Parental  EAAFEGCSKGKPFFGGDAVGYLDVTLGALVSWVHAGEALYGMRLFDATRSPLLDAWVDRFAALDAAKAAL
          E.A......GKPFFGGDA.G..DVTLG.......A.EAL.G.R..DA.R.PLL.AW..RF..LDAA...L
Retrocopy EGAL-AAAEGKPFFGGDAPGLVDVTLGSVIPRTRANEALTGTRVLDAARTPLLAAWAERFGELDAARKVL

Parental  PDAGRLAEYAKKR
          P..G...EY...R
Retrocopy PAVGDVVEYLETR

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Oryza rufipogon was not studied using RNA-Seq expression data.

ChIP-Seq

Oryza rufipogon was not studied using ChIP-Seq data.

EST

Oryza rufipogon was not studied using EST data.

TSS

Oryza rufipogon was not studied using FANTOM5 data.

Lab

retro_oruf_26 was not experimentally validated.

Homology

Retrocopy orthology:

Oryza rufipogon does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Oryza rufipogon	ORUFI10G17520	1 retrocopy	retro_oruf_26 ,